[gmx-users] disulphide bonds
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 27 02:33:52 CEST 2008
rams rams wrote:
> Hi,
>
> If I use -ignh, that will ignore all the hydrogens in my input. And
> these hydrogens are added by the gromacs.in <http://gromacs.in> the
> first step of creating the top file.
>
What is gromacs.in? Perhaps it would be best if you showed us, step by
step, what you are doing (with *exact* command lines).
Using pdb2gmx should be your first step, and using -ignh will indeed
ignore your hydrogen atoms, but it looks like they're named incorrectly
anyway, so that might be a good thing. Part of the function of pdb2gmx
is to add back the appropriate hydrogens according to residue templates,
so it's irrelevant what you have in the input; it's going to be replaced
with correct hydrogen atoms anyway.
-Justin
> Ram.
>
> On Thu, Jun 26, 2008 at 3:34 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> rams rams wrote:
>
> Dear Tsjerk,
>
> Thanks for the suggestion but when I use -merge command it
> says segmentation error. Let me put the problem in a more
> elaborated way.
>
> I am running this simulation on insulin. It has two chains "a"
> and "b" which are independent fragments but there are two
> inter disulphide bonds between the two chains. If I keep the
> two chains as a single molecule (as -merge command does)
> gromacs could recognize the inter dishlphide bonds but while
> running the following error appears:
>
> 396 398 113.3 0.1470 0.2974 0.1470
> 398 399 93.1 0.1530 0.4267 0.1530
> 399 400 45.5 0.1230 0.1693 0.1230
> 399 401 46.5 0.1330 0.1881 0.1330
> Step= 2, Dmax= 5.0e-03 nm, Epot= -3.06153e+22 Fmax=
> inf, atom= 25
> -------------------------------------------------------
> Program mdrun, VERSION 3.3.1
> Source code file: nsgrid.c, line: 226
>
> Range checking error:
> Explanation: During neighborsearching, we assign each particle
> to a grid
> based on its coordinates. If your system contains collisions
> or parameter
> errors that give particles very high velocities you might end
> up with some
> coordinates being +-Infinity or NaN (not-a-number). Obviously,
> we cannot
> put these on a grid, so this is usually where we detect those
> errors.
> Make sure your system is properly energy-minimized and that
> the potential
> energy seems reasonable before trying again.
>
> Variable ci has value -2147483648. It should have been within
> [ 0 .. 1000 ]
> Please report this to the mailing list (gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>)
>
>
> When do you get this error (i.e., minimization, equilibration,
> production)? Usually this type of error comes up from a poorly
> minimized/equilibrated structure.
> I agree with Tsjerk that using -merge is the right way to form
> your disulfide, so I assume something else is going wrong during
> your system preparation. If you'd like to provide details on what
> you're doing in terms of minimization/equilibration, and the
> contents of the relevant .mdp files, we may be able to detect
> problems.
>
> -Justin
>
> Where as, if I keep these two as separate molecules it couldnt
> recognize the two inter disulphide bonds but its running. Now
> it is adding hydrogens to the sulhur atoms.
>
> Is there any way to fix this problem ? Is there any way to
> edit the topology file to remove the added hydrogen atoms ?
>
> Thanks
> Ram.
>
> On Thu, Jun 26, 2008 at 10:26 AM, Tsjerk Wassenaar
> <tsjerkw at gmail.com <mailto:tsjerkw at gmail.com>
> <mailto:tsjerkw at gmail.com <mailto:tsjerkw at gmail.com>>> wrote:
>
> Hi Ram,
>
> Check the option -merge of pdb2gmx.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Jun 26, 2008 at 6:11 AM, rams rams
> <rams.crux at gmail.com <mailto:rams.crux at gmail.com>
> <mailto:rams.crux at gmail.com <mailto:rams.crux at gmail.com>>>
> wrote:
> > Dear Gromacs users,
> >
> > Is there any way to handle the disulphide bond formed
> between two
> > independent fragments of a protein ? Precisely it is an inter
> disulphide
> > bond between two fragments. If I keep the two fragments as
> separate objects
> > while preparing the pdb file (using TER between the two
> fragments), gromacs
> > is not asking for the formation of a disulphide bond. If
> I keep
> them as a
> > single object while preparing the input pdb, gromacs could
> recognize the
> > disulphide bond but while running the energy minimization its
> complaining
> > that the distances are too close.
> >
> > Is there any way to handle these ? I am also thinking
> like keep
> them as
> > separate objects and imposing positional restraints on
> both the
> sulphur
> > atoms. Is it all right to do that way ?
> >
> > Please suggest me some thing how to handle these ?
> >
> > Ram.
> >
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
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> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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